CS-327-1: Computational Methods in Biology
College of Arts & Sciences Syllabus
Bioinformatics is the discipline that applies mathematics, statistics, computer
science, chemistry, and biology to solving problems in biology using biological data sets.
The problems investigated are usually at the molecular level. These problems include sequence
alignment, genome assembly, models of evolution and phylogenetic trees, analyzing gene expression
data, and gene linkage analysis. One of the most important statistical tools used in bioinformatics
is the Bayesian network. This course introduces the techniques used in bioinformatics, in
particular Bayesian networks, and provides solutions to several bioinformatics problems.
CS-201 or MATH-251 (A grade of C or higher is required), BIO-100 or BIO-201
(A grade of C or higher is required), CS-200 (A grade of C or higher is required)
Monday/Wednesday 4:15 p.m. - 5:30 p.m.
Lech Walesa Hall 2054
Lech Walesa Hall 3049
Monday 5:45 p.m. - 6:45 p.m.
Wednesday 5:45 p.m. - 6:45 p.m.
Thursday 1:00 p.m. - 3:00 p.m.
Per university policy, grades may not be discussed via email.
All course-related questions should be posted on the D2L Discussion Forum.
Bioinformatics Algorithms An Active Learning Approach, 3rd Edition, ISBN: 978-0-9903746-3-3
- Grades, Homework Submissions (some assignments): D2L
- Discussion Forum: Piazza
- Course Lectures, Study Guides, Homework Assignments, Schedule: racheltrana/CS327_1.html
- Additional homework assignments: Rosalind
COURSE OBJECTIVES / STUDENT LEARNING OUTCOMES
Upon completing CS-327: Computational Methods in Biology, students will be able to:
- Apply computer science principles to solving problems in biology.
- Investigate some of the algorithmic ideas, such as dynamic programming and graph theory,
that are fundamental to an understanding of modern biology.
- Prepare students to work in the interdisciplinary area of recent advances in high-performance
computing and biology, especially with the massive information resources of the human
- Increase computational literacy.
- Understand the principles and some methods of genomics, gene expression and proteomics
that aid precision medicine, modern plant and animal breeding.
- Work with large, complicated datasets that once took researchers years to manually analyze.
- Introduction to Molecular Biology
- Introduction to Python
- Genome Replication: Transcription, Translation
- Sequencing Antibiotics
- Genome Alignment
- Genomic Data: Genome databases
- Genome Rearrangements
STUDENT TASKS / ASSIGNMENTS / REQUIREMENTS
Attendance is mandatory. More than six (6) absences will result in an automatic F in the course.
Homework will be assigned weekly, posted online. While working on homework
assignments with other students is encouraged, plagiarism is NOT tolerated. All work should
be unique. Students that submit duplicate/identical work will receive an F for that homework
assignment. All assignments must be submitted to D2L by the specified due date and time. There
are NO exceptions.
There will be several online (D2L) quizzes throughout the semester, designed to reinforce
core concepts in Programming II. These quizzes must be completed by the specified due date and
time (no extensions will be given).
Requirements for Graduate Students:
In addition to completing homework assignments and taking
the midterm and final exams, graduate students will be given a specific project topic within
the field of computational biology in which they will need to research and implement biological
algorithm. All work must be unique. Students that plagiarize on their project will receive an F for
the course. This will be graded as pass/fail. Graduate students that fail the project will drop a full
letter grade when calculating their final grade.
Grading Policies and Formulae:
|90 - 100 %
|80 - 89.99999999 %
|70 - 79.99999999 %
|60 - 69.99999999 %
|0 - 59.99999999 %
There will be a midterm exam, worth 37.5% of your final grade and a final exam, also
worth 37.5% of your final grade. The final exam date isWednesday, May 1 from 4:00 - 5:50 p.m.
This is set by the university final exam schedule, which is posted online. There are NO make-up
exams. The material in this course builds on itself and therefore the material for the exams is
implicitly cumulative. Exams are closed-book and closed-notes. Access to any digital devices is
UNIVERSITY POLICIES AND STATEMENTS
Academic Integrity Policy:
By enrolling in this course, you are bound by the
NEIU Student Code of Conduct
You will be informed by your instructor of any additional policy specific to your course regarding
plagiarism, class disruptions, etc.
Northeastern Illinois University (NEIU) complies with the Americans with Disabilities Act (ADA)
in making reasonable accommodations for qualified students with disabilities. To request accommodations,
students with special needs should make arrangements with the Student Disability Services
(SDS) office, located on the main campus in room D104. Contact SDS via (773) 442-4595
. It is your responsibility
to have the Accessibility Center send me this information by the 3rd week of the
COURSE POLICIES AND STATEMENTS
Attendance is mandatory. More than six (6) absences will result in an automatic
F in the course.
Submitting Assignments to D2L:
- Create a folder with your name and in that folder include all of your homework files (program
code, input and output files, but NO .class files).
- Compress the folder. For Windows: Right-click and choose “Send to” and then choose
"Compressed (zipped) Folder".
- Submit the zipped folder (.zip file) to D2L Dropbox.
- No grade of "I" will be given.
- No makeup exams or quizzes will be given. If you miss an exam or quiz, you will receive an
F for that exam/quiz.
- You must bring your NEIU ID to each exam, including the final exam. I reserve the right to
check your ID at each exam, including the final exam.
- The use of cell phones, iPads or computers during class time for non-class or non-emergency
purposes is not allowed. Phones are to be muted and laptops/iPads are to remain closed.
- There will be NO extra credit projects given to improve grades.
- Cheating and/or plagiarism will not be tolerated. Students that violate the NEIU academic
conduct policy may be subject to an F for that assignment, quiz, exam, project or any portion
(or all) of the final course grade
- Policies may be modified or added as I deem appropriate/necessary.
Monday, January 21, 2019: Martin Luther King, Jr. Birthday (No Classes)
Tuesday, February 12, 2019: Lincoln’s Birthday (No Classes)
Monday, March 18 - Sunday, March 24, 2019: Spring Break (No Classes)
Friday, March 29, 2019: Last day to drop with a W